The proliferation of open knowledge graphs has led to a surge in scholarly research on the topic over the past decade. This paper presents a bibliometric analysis of the scholarly literature on open knowledge graphs published between 2013 and 2023. The study aims to identify the trends, patterns, and impact of research in this field, as well as the key topics and research questions that have emerged. The work uses bibliometric techniques to analyze a sample of 4445 scholarly articles retrieved from Scopus. The findings reveal an ever-increasing number of publications on open knowledge graphs published every year, particularly in developed countries (+50 per year). These outputs are published in highly-referred scholarly journals and conferences. The study identifies three main research themes: (1) knowledge graph construction and enrichment, (2) evaluation and reuse, and (3) fusion of knowledge graphs into NLP systems. Within these themes, the study identifies specific tasks that have received considerable attention, including entity linking, knowledge graph embedding, and graph neural networks.
This work proposes a Physics-informed Neural Network framework with Graph Embedding (GPINN) to perform PINN in graph, i.e. topological space instead of traditional Euclidean space, for improved problem-solving efficiency. The method integrates topological data into the neural network's computations, which significantly boosts the performance of the Physics-Informed Neural Network (PINN). The graph embedding technique infuses extra dimensions into the input space to encapsulate the spatial characteristics of a graph while preserving the properties of the original space. The selection of these extra dimensions is guided by the Fiedler vector, offering an optimised pathologic notation of the graph. Two case studies are conducted, which demonstrate significant improvement in the performance of GPINN in comparison to traditional PINN, particularly in its superior ability to capture physical features of the solution.
Knowledge graph embedding models (KGEMs) have gained considerable traction in recent years. These models learn a vector representation of knowledge graph entities and relations, a.k.a. knowledge graph embeddings (KGEs). Learning versatile KGEs is desirable as it makes them useful for a broad range of tasks. However, KGEMs are usually trained for a specific task, which makes their embeddings task-dependent. In parallel, the widespread assumption that KGEMs actually create a semantic representation of the underlying entities and relations (e.g., project similar entities closer than dissimilar ones) has been challenged. In this work, we design heuristics for generating protographs -- small, modified versions of a KG that leverage RDF/S information. The learnt protograph-based embeddings are meant to encapsulate the semantics of a KG, and can be leveraged in learning KGEs that, in turn, also better capture semantics. Extensive experiments on various evaluation benchmarks demonstrate the soundness of this approach, which we call Modular and Agnostic SCHema-based Integration of protograph Embeddings (MASCHInE). In particular, MASCHInE helps produce more versatile KGEs that yield substantially better performance for entity clustering and node classification tasks. For link prediction, using MASCHinE substantially increases the number of semantically valid predictions with equivalent rank-based performance.
Inductive knowledge graph completion has been considered as the task of predicting missing triplets between new entities that are not observed during training. While most inductive knowledge graph completion methods assume that all entities can be new, they do not allow new relations to appear at inference time. This restriction prohibits the existing methods from appropriately handling real-world knowledge graphs where new entities accompany new relations. In this paper, we propose an INductive knowledge GRAph eMbedding method, InGram, that can generate embeddings of new relations as well as new entities at inference time. Given a knowledge graph, we define a relation graph as a weighted graph consisting of relations and the affinity weights between them. Based on the relation graph and the original knowledge graph, InGram learns how to aggregate neighboring embeddings to generate relation and entity embeddings using an attention mechanism. Experimental results show that InGram outperforms 14 different state-of-the-art methods on varied inductive learning scenarios.
Knowledge graphs are powerful tools for representing and organising complex biomedical data. Several knowledge graph embedding algorithms have been proposed to learn from and complete knowledge graphs. However, a recent study demonstrates the limited efficacy of these embedding algorithms when applied to biomedical knowledge graphs, raising the question of whether knowledge graph embeddings have limitations in biomedical settings. This study aims to apply state-of-the-art knowledge graph embedding models in the context of a recent biomedical knowledge graph, BioKG, and evaluate their performance and potential downstream uses. We achieve a three-fold improvement in terms of performance based on the HITS@10 score over previous work on the same biomedical knowledge graph. Additionally, we provide interpretable predictions through a rule-based method. We demonstrate that knowledge graph embedding models are applicable in practice by evaluating the best-performing model on four tasks that represent real-life polypharmacy situations. Results suggest that knowledge learnt from large biomedical knowledge graphs can be transferred to such downstream use cases. Our code is available at https://github.com/aryopg/biokge.
In the graph node embedding problem, embedding spaces can vary significantly for different data types, leading to the need for different GNN model types. In this paper, we model the embedding update of a node feature as a Hamiltonian orbit over time. Since the Hamiltonian orbits generalize the exponential maps, this approach allows us to learn the underlying manifold of the graph in training, in contrast to most of the existing literature that assumes a fixed graph embedding manifold with a closed exponential map solution. Our proposed node embedding strategy can automatically learn, without extensive tuning, the underlying geometry of any given graph dataset even if it has diverse geometries. We test Hamiltonian functions of different forms and verify the performance of our approach on two graph node embedding downstream tasks: node classification and link prediction. Numerical experiments demonstrate that our approach adapts better to different types of graph datasets than popular state-of-the-art graph node embedding GNNs. The code is available at \url{https://github.com/zknus/Hamiltonian-GNN}.
Finding meaningful representations and distances of hierarchical data is important in many fields. This paper presents a new method for hierarchical data embedding and distance. Our method relies on combining diffusion geometry, a central approach to manifold learning, and hyperbolic geometry. Specifically, using diffusion geometry, we build multi-scale densities on the data, aimed to reveal their hierarchical structure, and then embed them into a product of hyperbolic spaces. We show theoretically that our embedding and distance recover the underlying hierarchical structure. In addition, we demonstrate the efficacy of the proposed method and its advantages compared to existing methods on graph embedding benchmarks and hierarchical datasets.
Recent studies on automatic note generation have shown that doctors can save significant amounts of time when using automatic clinical note generation (Knoll et al., 2022). Summarization models have been used for this task to generate clinical notes as summaries of doctor-patient conversations (Krishna et al., 2021; Cai et al., 2022). However, assessing which model would best serve clinicians in their daily practice is still a challenging task due to the large set of possible correct summaries, and the potential limitations of automatic evaluation metrics. In this paper, we study evaluation methods and metrics for the automatic generation of clinical notes from medical conversations. In particular, we propose new task-specific metrics and we compare them to SOTA evaluation metrics in text summarization and generation, including: (i) knowledge-graph embedding-based metrics, (ii) customized model-based metrics, (iii) domain-adapted/fine-tuned metrics, and (iv) ensemble metrics. To study the correlation between the automatic metrics and manual judgments, we evaluate automatic notes/summaries by comparing the system and reference facts and computing the factual correctness, and the hallucination and omission rates for critical medical facts. This study relied on seven datasets manually annotated by domain experts. Our experiments show that automatic evaluation metrics can have substantially different behaviors on different types of clinical notes datasets. However, the results highlight one stable subset of metrics as the most correlated with human judgments with a relevant aggregation of different evaluation criteria.
A hyper-relational knowledge graph has been recently studied where a triplet is associated with a set of qualifiers; a qualifier is composed of a relation and an entity, providing auxiliary information for a triplet. While existing hyper-relational knowledge graph embedding methods assume that the entities are discrete objects, some information should be represented using numeric values, e.g., (J.R.R., was born in, 1892). Also, a triplet (J.R.R., educated at, Oxford Univ.) can be associated with a qualifier such as (start time, 1911). In this paper, we propose a unified framework named HyNT that learns representations of a hyper-relational knowledge graph containing numeric literals in either triplets or qualifiers. We define a context transformer and a prediction transformer to learn the representations based not only on the correlations between a triplet and its qualifiers but also on the numeric information. By learning compact representations of triplets and qualifiers and feeding them into the transformers, we reduce the computation cost of using transformers. Using HyNT, we can predict missing numeric values in addition to missing entities or relations in a hyper-relational knowledge graph. Experimental results show that HyNT significantly outperforms state-of-the-art methods on real-world datasets.
The main objective of Knowledge Graph (KG) embeddings is to learn low-dimensional representations of entities and relations, enabling the prediction of missing facts. A significant challenge in achieving better KG embeddings lies in capturing relation patterns, including symmetry, antisymmetry, inversion, commutative composition, non-commutative composition, hierarchy, and multiplicity. This study introduces a novel model called 3H-TH (3D Rotation and Translation in Hyperbolic space) that captures these relation patterns simultaneously. In contrast, previous attempts have not achieved satisfactory performance across all the mentioned properties at the same time. The experimental results demonstrate that the new model outperforms existing state-of-the-art models in terms of accuracy, hierarchy property, and other relation patterns in low-dimensional space, meanwhile performing similarly in high-dimensional space.
We propose KGT5-context, a simple sequence-to-sequence model for link prediction (LP) in knowledge graphs (KG). Our work expands on KGT5, a recent LP model that exploits textual features of the KG, has small model size, and is scalable. To reach good predictive performance, however, KGT5 relies on an ensemble with a knowledge graph embedding model, which itself is excessively large and costly to use. In this short paper, we show empirically that adding contextual information - i.e., information about the direct neighborhood of the query entity - alleviates the need for a separate KGE model to obtain good performance. The resulting KGT5-context model is simple, reduces model size significantly, and obtains state-of-the-art performance in our experimental study.
We consider a contrastive learning approach to knowledge graph embedding (KGE) via InfoNCE. For KGE, efficient learning relies on augmenting the training data with negative triples. However, most KGE works overlook the bias from generating the negative triples-false negative triples (factual triples missing from the knowledge graph). We argue that the generation of high-quality (i.e., hard) negative triples might lead to an increase in false negative triples. To mitigate the impact of false negative triples during the generation of hard negative triples, we propose the Hardness and Structure-aware (\textbf{HaSa}) contrastive KGE method, which alleviates the effect of false negative triples while generating the hard negative triples. Experiments show that HaSa improves the performance of InfoNCE-based KGE approaches and achieves state-of-the-art results in several metrics for WN18RR datasets and competitive results for FB15k-237 datasets compared to both classic and pre-trained LM-based KGE methods.
Graph representation learning models aim to represent the graph structure and its features into low-dimensional vectors in a latent space, which can benefit various downstream tasks, such as node classification and link prediction. Due to its powerful graph data modelling capabilities, various graph embedding models and libraries have been proposed to learn embeddings and help researchers ease conducting experiments. In this paper, we introduce a novel graph representation framework covering various graph embedding models, ranging from shallow to state-of-the-art models, namely Connector. First, we consider graph generation by constructing various types of graphs with different structural relations, including homogeneous, signed, heterogeneous, and knowledge graphs. Second, we introduce various graph representation learning models, ranging from shallow to deep graph embedding models. Finally, we plan to build an efficient open-source framework that can provide deep graph embedding models to represent structural relations in graphs. The framework is available at https://github.com/NSLab-CUK/Connector.
Negative sampling (NS) is widely used in knowledge graph embedding (KGE), which aims to generate negative triples to make a positive-negative contrast during training. However, existing NS methods are unsuitable when multi-modal information is considered in KGE models. They are also inefficient due to their complex design. In this paper, we propose Modality-Aware Negative Sampling (MANS) for multi-modal knowledge graph embedding (MMKGE) to address the mentioned problems. MANS could align structural and visual embeddings for entities in KGs and learn meaningful embeddings to perform better in multi-modal KGE while keeping lightweight and efficient. Empirical results on two benchmarks demonstrate that MANS outperforms existing NS methods. Meanwhile, we make further explorations about MANS to confirm its effectiveness.
This paper presents a framework for learning player embeddings in competitive games and events. Players and their win-loss relationships are modeled as a skill gap graph, which is an undirected weighted graph. The player embeddings are learned from the graph using a random walk-based graph embedding method and can reflect the relative skill levels among players. Embeddings are low-dimensional vector representations that can be conveniently applied to subsequent tasks while still preserving the topological relationships in a graph. In the latter part of this paper, Graphical Elo (GElo) is introduced as an application of player embeddings when rating player skills. GElo is an extension of the classic Elo rating system. It constructs a skill gap graph based on player match histories and learns player embeddings from it. Afterward, the rating scores that were calculated by Elo are adjusted according to player activeness and cosine similarities among player embeddings. GElo can be executed offline and in parallel, and it is non-intrusive to existing rating systems. Experiments on public datasets show that GElo makes a more reliable evaluation of player skill levels than vanilla Elo. The experimental results suggest potential applications of player embeddings in competitive games and events.
In this paper, we introduce a method called graph fusion embedding, designed for multi-graph embedding with shared vertex sets. Under the framework of supervised learning, our method exhibits a remarkable and highly desirable synergistic effect: for sufficiently large vertex size, the accuracy of vertex classification consistently benefits from the incorporation of additional graphs. We establish the mathematical foundation for the method, including the asymptotic convergence of the embedding, a sufficient condition for asymptotic optimal classification, and the proof of the synergistic effect for vertex classification. Our comprehensive simulations and real data experiments provide compelling evidence supporting the effectiveness of our proposed method, showcasing the pronounced synergistic effect for multiple graphs from disparate sources.
Several approaches have been developed that generate embeddings for Description Logic ontologies and use these embeddings in machine learning. One approach of generating ontologies embeddings is by first embedding the ontologies into a graph structure, i.e., introducing a set of nodes and edges for named entities and logical axioms, and then applying a graph embedding to embed the graph in $\mathbb{R}^n$. Methods that embed ontologies in graphs (graph projections) have different formal properties related to the type of axioms they can utilize, whether the projections are invertible or not, and whether they can be applied to asserted axioms or their deductive closure. We analyze, qualitatively and quantitatively, several graph projection methods that have been used to embed ontologies, and we demonstrate the effect of the properties of graph projections on the performance of predicting axioms from ontology embeddings. We find that there are substantial differences between different projection methods, and both the projection of axioms into nodes and edges as well ontological choices in representing knowledge will impact the success of using ontology embeddings to predict axioms.
Graph embedding maps graph nodes to low-dimensional vectors, and is widely adopted in machine learning tasks. The increasing availability of billion-edge graphs underscores the importance of learning efficient and effective embeddings on large graphs, such as link prediction on Twitter with over one billion edges. Most existing graph embedding methods fall short of reaching high data scalability. In this paper, we present a general-purpose, distributed, information-centric random walk-based graph embedding framework, DistGER, which can scale to embed billion-edge graphs. DistGER incrementally computes information-centric random walks. It further leverages a multi-proximity-aware, streaming, parallel graph partitioning strategy, simultaneously achieving high local partition quality and excellent workload balancing across machines. DistGER also improves the distributed Skip-Gram learning model to generate node embeddings by optimizing the access locality, CPU throughput, and synchronization efficiency. Experiments on real-world graphs demonstrate that compared to state-of-the-art distributed graph embedding frameworks, including KnightKing, DistDGL, and Pytorch-BigGraph, DistGER exhibits 2.33x-129x acceleration, 45% reduction in cross-machines communication, and > 10% effectiveness improvement in downstream tasks.
In this work, we present an end-to-end Knowledge Graph Question Answering (KGQA) system named GETT-QA. GETT-QA uses T5, a popular text-to-text pre-trained language model. The model takes a question in natural language as input and produces a simpler form of the intended SPARQL query. In the simpler form, the model does not directly produce entity and relation IDs. Instead, it produces corresponding entity and relation labels. The labels are grounded to KG entity and relation IDs in a subsequent step. To further improve the results, we instruct the model to produce a truncated version of the KG embedding for each entity. The truncated KG embedding enables a finer search for disambiguation purposes. We find that T5 is able to learn the truncated KG embeddings without any change of loss function, improving KGQA performance. As a result, we report strong results for LC-QuAD 2.0 and SimpleQuestions-Wikidata datasets on end-to-end KGQA over Wikidata.
In this paper, we propose a novel model called SGFormer, Semantic Graph TransFormer for point cloud-based 3D scene graph generation. The task aims to parse a point cloud-based scene into a semantic structural graph, with the core challenge of modeling the complex global structure. Existing methods based on graph convolutional networks (GCNs) suffer from the over-smoothing dilemma and can only propagate information from limited neighboring nodes. In contrast, SGFormer uses Transformer layers as the base building block to allow global information passing, with two types of newly-designed layers tailored for the 3D scene graph generation task. Specifically, we introduce the graph embedding layer to best utilize the global information in graph edges while maintaining comparable computation costs. Furthermore, we propose the semantic injection layer to leverage linguistic knowledge from large-scale language model (i.e., ChatGPT), to enhance objects' visual features. We benchmark our SGFormer on the established 3DSSG dataset and achieve a 40.94% absolute improvement in relationship prediction's R@50 and an 88.36% boost on the subset with complex scenes over the state-of-the-art. Our analyses further show SGFormer's superiority in the long-tail and zero-shot scenarios. Our source code is available at https://github.com/Andy20178/SGFormer.